Countering al-Shabab: How the War on Terrorism Is Being Fought in East Africa

Two bombings of churches in Kenya pointed to the resurgence al-Qaeda-linked terrorist groups in East Africa. But a TIME investigation into how the region's countries (and the U.S.) are handling groups like Somalia's al-Shabab leads to accusations of illegal, murky tactics

The efforts of Margulies and others made Guantánamo a legal nightmare for the U.S. The Kampala investigation represents the counterterrorism community’s response: if Africa counterterrorism operations are run by Africans and kept inside Africa, with Americans officially present only as advisers and observers, Margulies and others will find it much harder to sue the U.S. “If these people are not in U.S. custody, then, simply, there is no jurisdiction,” says Margulies. Western intelligence work in East Africa is “an experiment, an evolution — Counterterrorism 2.0,” he says. “It’s very deliberate and reflects a learning curve from the perceived mistakes of Counterterrorism 1.0.”

But rendition is still illegal. Which begs a crucial question: To what extent is the U.S. running the East Africa operations? U.S. Ambassador Lanier says of the U.S. role in the Kampala investigations: “The FBI came in here for a few weeks. We were very involved in that investigation. We participated in the accumulation of evidence. What they chose to do with that information … We are not part of the arrest and prosecution of anybody.”

But while there is no suggestion that U.S. agents physically organized the rendition operations, statements from several of the Kampala accused unanimously indicate that the U.S. (and some British intelligence officers) did run the subsequent interrogations. According to those questioned, Western and Ugandan officers also frequently told their prisoners that the foreigners were in charge. Walubiri is adamant that the U.S. took the lead. “On the face of it, it looks like a very noble, lawful and helpful intervention — training our police, security-services and intelligence agencies,” he says. “What they are actually doing is assisting the Ugandan and Kenyan governments to break laws on extradition and pretrial detention, and against the torture and mistreatment of prisoners; to deny the accused access to next of kin, lawyers or doctors; to frustrate attempts to get bail; and in setting up a kangaroo court. They are trying to run a Guantánamo in Uganda, with the cover that the Ugandan government is doing it. To whom are they accountable?” Margulies shares Walubiri’s concerns. “The traction we got with Counterterrorism 1.0 was precisely because it was visible. If it’s completely hidden, then who knows what’s happening? Democracy dies in the dark,” he says.

This picture of a secret and illegal Western-dominated intelligence operation also conforms to established patterns of Western counterterrorism in East Africa. Previous investigations by al-Kimathi, Gutteridge, the British rights group Reprieve, and TIME and other media, have revealed the existence since at least 2006 of a cooperative network of security and intelligence services linking Kenya, Uganda, Ethiopia and Somalia, overseen by U.S. and British personnel. Its modus operandi is rendition, secret prisons and torture. These were the same methods used in the aftermath of the 1998 bombings when two suspects, Mohammed Saddiq Odeh and Mohammed Rashed al-‘Owhali, were renditioned from Kenya to the U.S. After that, anecdotal evidence suggests rendition became routine for U.S. intelligence in East Africa. In 2003 a Tanzanian, Suleiman Abdallah Salim, was taken from Somalia to Bagram, Afghanistan, and held there for five years; a Kenyan, Abdulmalik Mohammed, was taken from Mombasa to Guantánamo in 2007; another Kenyan, Ahmed Abdullahi Hassan, was taken from Nairobi to a secret prison in Mogadishu in 2009. After the 2006 Ethiopian invasion of Somalia, TIME reported how U.S. Special Operations forces and the CIA sifted the ranks of captured Islamists corralled in southern Somalia for possible al-Qaeda members. Of these, Reprieve and others documented that 85 to 120 suspects (at least 11 of them children) were detained on the Kenya-Somalia border, moved to a secret prison in Mogadishu and finally to another prison in Ethiopia, all the while interrogated by British and American intelligence. In seven years in East Africa before she herself was deported from Kenya in 2011, Gutteridge says she documented well over 100 cases of rendition.

For the U.S. and its allies, AMISOM represents progress in the war on terrorism. Rather than mass deployment of troops, the U.S. and the E.U. are funding countries to tackle their own regional issues. For Africans, that is proof of an increasingly self-reliant continent. For the West, that means less loss of life, less expense and less risk of blowback from the Muslim world.

But the evidence gathered by TIME appears to show that, for the intelligence services, cooperating with African security services is intended not to empower African counterterrorism but merely to avoid scrutiny. The black-site prisons continue. So, as Abdow’s story illustrates, do the abuses. And, as recent history shows, a community that perceives itself under close watch, even oppressed, by African and Western security services is liable to grow more radical.

Ominously, that seems to be occurring. East Africa, previously a place of mostly harmonious religious diversity, is starting to see a new hard division between Christians and Muslims. Muslims, the minority, are denigrated and abused by the police, media and in general conversation. Some are reacting badly. A U.N. report last July found al-Shabab had already built an extensive funding, recruiting and training network in Kenya. On Jan. 15 this year, the Kenya-based Muslim Youth Center declared its head, Amiir Ahmad Iman Ali, al-Shabab’s leader in Kenya. “Jihad should now be waged inside Kenya,” Ali added. As Sunday’s attacks suggest, it now is.